title: Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
abstract: Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole-root and cell-type-specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified 918 additional cis-NAT pairs. Newly identified cis-NAT pairs are supported by polyadenylation data, alternative splicing patterns, and RT-PCR validation. We found 209 cis-NAT pairs that have opposite expression levels in neighboring cell types, implying cell-type-specific roles for cis-NATs. By integrating a genome-wide epigenetic profile of Arabidopsis, we identified a unique chromatin signature of cis-NATs, suggesting a connection between cis-NAT transcription and chromatin modification in plants. An analysis of small-RNA sequencing data showed that ∼4% of cis-NAT pairs produce putative cis-NAT-induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs.
authors.affiliation: Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.forename: Louisa M
authors.initials: LM
authors.lastname: Liberman
authors.forename: Neelanjan
authors.initials: N
authors.lastname: Mukherjee
authors.forename: Philip N
authors.initials: PN
authors.lastname: Benfey
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D057890:Epigenomics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D026723:Polyadenylation; D034622:RNA Interference; D016372:RNA, Antisense / Q000032:analysis / Q000235:genetics*; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering